else:
alniter = sam.fetch(until_eof=True)
for aln in alniter:
# print aln.pos, dir(aln)
nr+=1
if nr%200000 == 0:
sys.stderr.write("%d\n"%nr)
i,j = aln.tid, aln.rnext
if args.debug: print([i,j,int(aln.mapq),aln.tlen,aln.is_duplicate])
if int(aln.mapq) < args.min_qual: continue
if BamTags.mate_mapq(aln) < args.min_qual: continue
if aln.is_duplicate : continue
if args.junctions and BamTags.junction(aln) != "T": continue
if i==j:
if (slen[i]<args.minlength) : continue
if aln.tlen < 0: continue
hist[aln.tlen] = hist.get(aln.tlen,0)+1
n+=1
else:
if (slen[i]<args.minlength) or (slen[j]<args.minlength) : continue
if not aln.is_read1: continue
x = min( aln.pos , slen[i] - aln.pos ) + min( aln.pnext,slen[j]-aln.pnext)
hist2[x] = hist2.get(x,0)+1
n2+=1
if args.head and (n+n2)>args.head:
break
